Published in BMC Genomics on May 20, 2008
Horizontal gene transfer in evolution: facts and challenges. Proc Biol Sci (2009) 1.65
Inferring genomic flux in bacteria. Genome Res (2008) 1.25
Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS One (2013) 1.23
Inference and characterization of horizontally transferred gene families using stochastic mapping. Mol Biol Evol (2009) 1.23
Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony--a simulation study. Genome Biol Evol (2011) 0.98
On the need for widespread horizontal gene transfers under genome size constraint. Biol Direct (2009) 0.92
Inferring horizontal gene transfer. PLoS Comput Biol (2015) 0.88
Does gene translocation accelerate the evolution of laterally transferred genes? Genetics (2009) 0.86
Rhizome of life, catastrophes, sequence exchanges, gene creations, and giant viruses: how microbial genomics challenges Darwin. Front Cell Infect Microbiol (2012) 0.83
How microbiology helps define the rhizome of life. Front Cell Infect Microbiol (2012) 0.82
Inferring bacterial genome flux while considering truncated genes. Genetics (2010) 0.80
Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past. Genome Biol Evol (2013) 0.80
On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations. BMC Evol Biol (2010) 0.78
DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood. BMC Bioinformatics (2014) 0.78
Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling. Evol Bioinform Online (2012) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (2001) 101.31
A genomic perspective on protein families. Science (1997) 50.51
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol (1994) 24.04
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol (1992) 11.19
Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature (2003) 10.73
Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol (1997) 9.50
Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A (1999) 7.65
Prokaryotic evolution in light of gene transfer. Mol Biol Evol (2002) 6.53
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol (2000) 6.50
Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet (2005) 6.47
Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol (2005) 5.21
Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res (2002) 4.85
Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep (2001) 4.78
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol (2003) 4.70
Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science (2006) 4.60
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet (2005) 4.19
Animal evolution and the molecular signature of radiations compressed in time. Science (2005) 3.98
Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res (2000) 3.95
The genetic core of the universal ancestor. Genome Res (2003) 3.82
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol (2005) 3.74
Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci U S A (1998) 3.72
Phylogenetics and the cohesion of bacterial genomes. Science (2003) 3.61
Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet (2002) 3.44
H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog (2006) 3.29
Evolutionary dynamics of full genome content in Escherichia coli. EMBO J (2000) 2.86
Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol (2004) 2.74
Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res (2006) 2.46
The balance of driving forces during genome evolution in prokaryotes. Genome Res (2003) 2.39
Clann: investigating phylogenetic information through supertree analyses. Bioinformatics (2004) 2.36
Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol (2003) 2.27
Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res (2004) 2.14
Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol (2005) 2.10
Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc Biol Sci (2004) 2.05
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci U S A (2007) 1.96
Different evolutionary patterns between young duplicate genes in the human genome. Genome Biol (2003) 1.92
The source of laterally transferred genes in bacterial genomes. Genome Biol (2003) 1.87
The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet (2000) 1.82
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora. J Bacteriol (2005) 1.77
The fate of laterally transferred genes: life in the fast lane to adaptation or death. Genome Res (2006) 1.66
Integration of horizontally transferred genes into regulatory interaction networks takes many million years. Mol Biol Evol (2007) 1.56
Insights on biology and evolution from microbial genome sequencing. Genome Res (2005) 1.54
Large-scale sequencing and the new animal phylogeny. Trends Ecol Evol (2006) 1.45
Why are the genomes of endosymbiotic bacteria so stable? Trends Genet (2003) 1.36
Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes. Genome Biol (2002) 1.35
Duplication is more common among laterally transferred genes than among indigenous genes. Genome Biol (2003) 1.34
Taking variation of evolutionary rates between sites into account in inferring phylogenies. J Mol Evol (2001) 1.32
A phylogenomic study of endosymbiotic bacteria. Mol Biol Evol (2004) 1.26
Patterns of bacterial gene movement. Mol Biol Evol (2004) 1.20
The role of laterally transferred genes in adaptive evolution. BMC Evol Biol (2007) 1.18
Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes. Mol Biol Evol (2004) 1.16
16S rRNA phylogeny of sponge-associated cyanobacteria. Appl Environ Microbiol (2005) 1.13
Complexity, connectivity, and duplicability as barriers to lateral gene transfer. Genome Biol (2007) 1.13
Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis. Mol Biol Evol (2004) 1.11
The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process. Mol Biol Evol (2006) 1.10
Lack of evidence for horizontal transfer of the lac operon into Escherichia coli. Mol Biol Evol (2004) 0.94
Systematic overestimation of gene gain through false diagnosis of gene absence. Genome Biol (2007) 0.85
High rates of lateral gene transfer are not due to false diagnosis of gene absence. Gene (2008) 0.82
Can biochemical properties serve as selective pressure for gene selection during inter-species and endosymbiotic lateral gene transfer? Syst Biol (Stevenage) (2006) 0.78
Antibiotic resistance is ancient. Nature (2011) 4.83
A draft genome of Yersinia pestis from victims of the Black Death. Nature (2011) 3.18
Pervasive cryptic epistasis in molecular evolution. PLoS Genet (2010) 2.19
A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups. Syst Biol (2007) 1.70
The fate of laterally transferred genes: life in the fast lane to adaptation or death. Genome Res (2006) 1.66
Transcriptional profiling implicates novel interactions between abiotic stress and hormonal responses in Thellungiella, a close relative of Arabidopsis. Plant Physiol (2006) 1.62
Problems with co-funding in Canada. Science (2005) 1.48
The selective cause of an ancient adaptation. Science (2005) 1.45
Simple sequences are rare in the Protein Data Bank. Proteins (2002) 1.34
Gene gain and gene loss in streptococcus: is it driven by habitat? Mol Biol Evol (2006) 1.31
Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons? New Phytol (2011) 1.23
The role of laterally transferred genes in adaptive evolution. BMC Evol Biol (2007) 1.18
The pattern of amino acid replacements in alpha/beta-barrels. Mol Biol Evol (2002) 1.16
Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849. N Engl J Med (2014) 1.16
A non-long terminal repeat retrotransposon family is restricted to the germ line micronucleus of the ciliated protozoan Tetrahymena thermophila. Eukaryot Cell (2004) 1.12
Assigning sequences to species in the absence of large interspecific differences. Mol Phylogenet Evol (2010) 1.12
An integrated approach to functional genomics: construction of a novel reporter gene fusion library for Sinorhizobium meliloti. Appl Environ Microbiol (2006) 1.10
Genome-wide evidence for selection acting on single amino acid repeats. Genome Res (2010) 1.00
Low-complexity sequences and single amino acid repeats: not just "junk" peptide sequences. Genome (2010) 0.99
Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error. PLoS One (2012) 0.95
A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history. Can J Microbiol (2003) 0.93
Dinucleotide compositional analysis of Sinorhizobium meliloti using the genome signature: distinguishing chromosomes and plasmids. Funct Integr Genomics (2002) 0.92
Gene amelioration demonstrated: the journey of nascent genes in bacteria. Genome (2008) 0.92
Selection and slippage creating serine homopolymers. Mol Biol Evol (2006) 0.91
Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis. Can J Microbiol (2006) 0.89
The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti. Microbiology (2011) 0.87
Does gene translocation accelerate the evolution of laterally transferred genes? Genetics (2009) 0.86
Asymmetrical evolution of cytochrome bd subunits. J Mol Evol (2006) 0.86
Identification of conflicting selective effects on highly expressed genes. Evol Bioinform Online (2007) 0.84
Neurological proteins are not enriched for repetitive sequences. Genetics (2004) 0.83
The evolution of the class A scavenger receptors. BMC Evol Biol (2012) 0.83
"Patchy-tachy" leads to false positives for recombination. Mol Biol Evol (2011) 0.82
High rates of lateral gene transfer are not due to false diagnosis of gene absence. Gene (2008) 0.82
Increased polymorphism near low-complexity sequences across the genomes of Plasmodium falciparum isolates. Genome Biol Evol (2011) 0.82
RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions. BMC Genomics (2013) 0.80
Inferring bacterial genome flux while considering truncated genes. Genetics (2010) 0.80
Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity. BMC Plant Biol (2012) 0.79
Nucleotide substitution bias within the genus Drosophila affects the pattern of proteome evolution. Genome Biol Evol (2009) 0.78
Inferring sequence regions under functional divergence in duplicate genes. Bioinformatics (2011) 0.78
Simple sequence in brain and nervous system specific proteins. Genome (2005) 0.77
The effect of sampling from subdivided populations on species identification with DNA barcodes using a Bayesian statistical approach. Mol Phylogenet Evol (2012) 0.76
Increased substitution rates surrounding low-complexity regions within primate proteins. Genome Biol Evol (2014) 0.76
Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility. Mol Ecol Resour (2013) 0.76
Efficient algorithms for counting and reporting segregating sites in genomic sequences. J Comput Biol (2007) 0.75